Identification of differentially expressed genes for Pseudomonas sp. Cr13 stimulated by hexavalent chromium
Over exploitation of mineral resources has increasingly caused serious heavy metal contamination such as chromium (Cr). Cr(VI), the pathogenicity factor, is one of common environmental contaminants and widely known health hazards to living organisms. Therefore, it is urgent to control the polluted s...
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| Veröffentlicht in: | PloS one 2022-08, Vol.17 (8), p.e0272528-e0272528 |
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| description | Over exploitation of mineral resources has increasingly caused serious heavy metal contamination such as chromium (Cr). Cr(VI), the pathogenicity factor, is one of common environmental contaminants and widely known health hazards to living organisms. Therefore, it is urgent to control the polluted soil. Up to now, little is known about the regulatory mechanisms of Cr response in Pseudomonas sp. Cr13. In this study, transcriptome and differentially expressed genes in Pseudomonas sp. Cr13 strain was characterized by a comparison between Cr(VI)-treated sample and control sample using transcriptome sequencing approach. In total, 2974 genes were annotated, including 1245 (1154 down-regulated genes and 91 up-regulated genes) differentially expressed genes (DEGs). All DEGs could be assigned to 29 pathways, of which pathways related to amino acid metabolism, carbohydrate metabolism, energy metabolism and signal transduction mechanism were significantly enriched in Pseudomonas sp. Cr13. A possible mechanism for Cr toxicity response might be an active efflux which utilized a heavy metal translocating P-type ATPase to lower the intracellular Cr concentration. The down-regulated genes related to the antioxidant defense system had a key role in Cr reduction, such as SodA, Gst, osmC, BtuE, KatE, csdA and AhpC. The proteins that were visibly up-regulated, were likely to involve in alleviating Cr(VI) stress, and the significantly down-regulated genes such as MarR, Lrp, FhlA, GntR, HrcA, LysR family genes, were likely to reduce Cr(VI) induced oxidative stress. In addition, real-time quantitative PCR was used to analyze the expression patterns of some Cr responsive genes. This study reported the first identification of Cr responsive genes, and inferred the underlying regulatory mechanisms of response to Cr(VI) stress in Pseudomonas sp. Cr13. |
| doi_str_mv | 10.1371/journal.pone.0272528 |
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Cr13 stimulated by hexavalent chromium</title><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><source>Public Library of Science (PLoS)</source><creator>Pang, Bingbing ; Yu, Hongling ; Zhang, Jin ; Ye, Fengcai ; Wu, Haifeng ; Shang, Changhua</creator><creatorcontrib>Pang, Bingbing ; Yu, Hongling ; Zhang, Jin ; Ye, Fengcai ; Wu, Haifeng ; Shang, Changhua</creatorcontrib><description>Over exploitation of mineral resources has increasingly caused serious heavy metal contamination such as chromium (Cr). Cr(VI), the pathogenicity factor, is one of common environmental contaminants and widely known health hazards to living organisms. Therefore, it is urgent to control the polluted soil. Up to now, little is known about the regulatory mechanisms of Cr response in Pseudomonas sp. Cr13. In this study, transcriptome and differentially expressed genes in Pseudomonas sp. Cr13 strain was characterized by a comparison between Cr(VI)-treated sample and control sample using transcriptome sequencing approach. In total, 2974 genes were annotated, including 1245 (1154 down-regulated genes and 91 up-regulated genes) differentially expressed genes (DEGs). All DEGs could be assigned to 29 pathways, of which pathways related to amino acid metabolism, carbohydrate metabolism, energy metabolism and signal transduction mechanism were significantly enriched in Pseudomonas sp. Cr13. A possible mechanism for Cr toxicity response might be an active efflux which utilized a heavy metal translocating P-type ATPase to lower the intracellular Cr concentration. The down-regulated genes related to the antioxidant defense system had a key role in Cr reduction, such as SodA, Gst, osmC, BtuE, KatE, csdA and AhpC. The proteins that were visibly up-regulated, were likely to involve in alleviating Cr(VI) stress, and the significantly down-regulated genes such as MarR, Lrp, FhlA, GntR, HrcA, LysR family genes, were likely to reduce Cr(VI) induced oxidative stress. In addition, real-time quantitative PCR was used to analyze the expression patterns of some Cr responsive genes. This study reported the first identification of Cr responsive genes, and inferred the underlying regulatory mechanisms of response to Cr(VI) stress in Pseudomonas sp. 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This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Cr13 stimulated by hexavalent chromium</title><title>PloS one</title><description>Over exploitation of mineral resources has increasingly caused serious heavy metal contamination such as chromium (Cr). Cr(VI), the pathogenicity factor, is one of common environmental contaminants and widely known health hazards to living organisms. Therefore, it is urgent to control the polluted soil. Up to now, little is known about the regulatory mechanisms of Cr response in Pseudomonas sp. Cr13. In this study, transcriptome and differentially expressed genes in Pseudomonas sp. Cr13 strain was characterized by a comparison between Cr(VI)-treated sample and control sample using transcriptome sequencing approach. In total, 2974 genes were annotated, including 1245 (1154 down-regulated genes and 91 up-regulated genes) differentially expressed genes (DEGs). All DEGs could be assigned to 29 pathways, of which pathways related to amino acid metabolism, carbohydrate metabolism, energy metabolism and signal transduction mechanism were significantly enriched in Pseudomonas sp. Cr13. A possible mechanism for Cr toxicity response might be an active efflux which utilized a heavy metal translocating P-type ATPase to lower the intracellular Cr concentration. The down-regulated genes related to the antioxidant defense system had a key role in Cr reduction, such as SodA, Gst, osmC, BtuE, KatE, csdA and AhpC. The proteins that were visibly up-regulated, were likely to involve in alleviating Cr(VI) stress, and the significantly down-regulated genes such as MarR, Lrp, FhlA, GntR, HrcA, LysR family genes, were likely to reduce Cr(VI) induced oxidative stress. In addition, real-time quantitative PCR was used to analyze the expression patterns of some Cr responsive genes. This study reported the first identification of Cr responsive genes, and inferred the underlying regulatory mechanisms of response to Cr(VI) stress in Pseudomonas sp. Cr13.</description><subject>Amino acids</subject><subject>Analysis</subject><subject>Antioxidants</subject><subject>Biology and Life Sciences</subject><subject>Bioremediation</subject><subject>Carbohydrate metabolism</subject><subject>Carbohydrates</subject><subject>Chromium</subject><subject>Contaminants</subject><subject>Contamination</subject><subject>DNA testing</subject><subject>Efficiency</subject><subject>Efflux</subject><subject>Energy metabolism</subject><subject>Enzymes</subject><subject>Exploitation</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Health aspects</subject><subject>Health hazards</subject><subject>Heavy metals</subject><subject>Hexavalent chromium</subject><subject>Kinases</subject><subject>Laboratories</subject><subject>Medicine and Health Sciences</subject><subject>Metabolism</subject><subject>Metals</subject><subject>Microorganisms</subject><subject>Mineral resources</subject><subject>Oxidative stress</subject><subject>Pathogenicity</subject><subject>Pathogens</subject><subject>Pathways</subject><subject>Physical Sciences</subject><subject>Physiology</subject><subject>Pollution control</subject><subject>Pseudomonas</subject><subject>R&D</subject><subject>Regulatory mechanisms (biology)</subject><subject>Research & development</subject><subject>Resource exploitation</subject><subject>Sediment pollution</subject><subject>Signal transduction</subject><subject>Soil contamination</subject><subject>Soil pollution</subject><subject>Toxicity</subject><subject>Transcriptomes</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNptkl2L1DAUhoso7of-A8GAIN7MeJI0SXsjLIOuAwt6odchTU9mMqbNmLTLzr-341TZEa8SkofnfPAWxSsKS8oVfb-LY-pNWO5jj0tgiglWPSkuac3ZQjLgTx_dL4qrnHcAgldSPi8uuKg5SKgvix_rFvvBO2_N4GNPoiOtdw7T8dWEcCD4sE-YM7Zkgz1m4mIiXzOObexibzLJ-yVZJcpJHnw3BjNMZHMgW3ww9yZMGmK3KXZ-7F4Uz5wJGV_O53Xx_dPHb6vPi7svt-vVzd3CCsmGhUNkALJpDJclCqVaDso0AmsGZekUttI6oACtkWApc9YqqBVwx3ilrOPXxeuTdx9i1vOesmayrqGqBOMTsT4RbTQ7vU--M-mgo_H690NMG23S4G1AXfKqtQilc5KVFFjjpDClKAEb7ijSyfVhrjY2HU5sPyQTzqTnP73f6k281zUXglZqErybBSn-HDEPuvPZYgimxzie-lZQ1nU9oW_-Qf8_3Uxtpv1r37s41bVHqb5RlEnJmKwm6u0jaosmDNscw3iMQT4HyxNoU8w5ofs7GwV9jOKfJvQxinqOIv8FBDnSkg</recordid><startdate>20220805</startdate><enddate>20220805</enddate><creator>Pang, Bingbing</creator><creator>Yu, Hongling</creator><creator>Zhang, Jin</creator><creator>Ye, Fengcai</creator><creator>Wu, Haifeng</creator><creator>Shang, Changhua</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PHGZM</scope><scope>PHGZT</scope><scope>PIMPY</scope><scope>PJZUB</scope><scope>PKEHL</scope><scope>PPXIY</scope><scope>PQEST</scope><scope>PQGLB</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0003-1447-6117</orcidid></search><sort><creationdate>20220805</creationdate><title>Identification of differentially expressed genes for Pseudomonas sp. Cr13 stimulated by hexavalent chromium</title><author>Pang, Bingbing ; Yu, Hongling ; Zhang, Jin ; Ye, Fengcai ; Wu, Haifeng ; Shang, Changhua</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c562t-fee2006bba364e577d307ab5e92044f7ed6cf0100da60c12fcc709703f2387cf3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Amino acids</topic><topic>Analysis</topic><topic>Antioxidants</topic><topic>Biology and Life Sciences</topic><topic>Bioremediation</topic><topic>Carbohydrate metabolism</topic><topic>Carbohydrates</topic><topic>Chromium</topic><topic>Contaminants</topic><topic>Contamination</topic><topic>DNA testing</topic><topic>Efficiency</topic><topic>Efflux</topic><topic>Energy metabolism</topic><topic>Enzymes</topic><topic>Exploitation</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Health aspects</topic><topic>Health hazards</topic><topic>Heavy metals</topic><topic>Hexavalent chromium</topic><topic>Kinases</topic><topic>Laboratories</topic><topic>Medicine and Health Sciences</topic><topic>Metabolism</topic><topic>Metals</topic><topic>Microorganisms</topic><topic>Mineral resources</topic><topic>Oxidative stress</topic><topic>Pathogenicity</topic><topic>Pathogens</topic><topic>Pathways</topic><topic>Physical Sciences</topic><topic>Physiology</topic><topic>Pollution control</topic><topic>Pseudomonas</topic><topic>R&D</topic><topic>Regulatory mechanisms (biology)</topic><topic>Research & development</topic><topic>Resource exploitation</topic><topic>Sediment pollution</topic><topic>Signal transduction</topic><topic>Soil contamination</topic><topic>Soil pollution</topic><topic>Toxicity</topic><topic>Transcriptomes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pang, Bingbing</creatorcontrib><creatorcontrib>Yu, Hongling</creatorcontrib><creatorcontrib>Zhang, Jin</creatorcontrib><creatorcontrib>Ye, Fengcai</creatorcontrib><creatorcontrib>Wu, Haifeng</creatorcontrib><creatorcontrib>Shang, Changhua</creatorcontrib><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection (ProQuest)</collection><collection>Natural Science Collection (ProQuest)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Pang, Bingbing</au><au>Yu, Hongling</au><au>Zhang, Jin</au><au>Ye, Fengcai</au><au>Wu, Haifeng</au><au>Shang, Changhua</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of differentially expressed genes for Pseudomonas sp. Cr13 stimulated by hexavalent chromium</atitle><jtitle>PloS one</jtitle><date>2022-08-05</date><risdate>2022</risdate><volume>17</volume><issue>8</issue><spage>e0272528</spage><epage>e0272528</epage><pages>e0272528-e0272528</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Over exploitation of mineral resources has increasingly caused serious heavy metal contamination such as chromium (Cr). Cr(VI), the pathogenicity factor, is one of common environmental contaminants and widely known health hazards to living organisms. Therefore, it is urgent to control the polluted soil. Up to now, little is known about the regulatory mechanisms of Cr response in Pseudomonas sp. Cr13. In this study, transcriptome and differentially expressed genes in Pseudomonas sp. Cr13 strain was characterized by a comparison between Cr(VI)-treated sample and control sample using transcriptome sequencing approach. In total, 2974 genes were annotated, including 1245 (1154 down-regulated genes and 91 up-regulated genes) differentially expressed genes (DEGs). All DEGs could be assigned to 29 pathways, of which pathways related to amino acid metabolism, carbohydrate metabolism, energy metabolism and signal transduction mechanism were significantly enriched in Pseudomonas sp. Cr13. A possible mechanism for Cr toxicity response might be an active efflux which utilized a heavy metal translocating P-type ATPase to lower the intracellular Cr concentration. The down-regulated genes related to the antioxidant defense system had a key role in Cr reduction, such as SodA, Gst, osmC, BtuE, KatE, csdA and AhpC. The proteins that were visibly up-regulated, were likely to involve in alleviating Cr(VI) stress, and the significantly down-regulated genes such as MarR, Lrp, FhlA, GntR, HrcA, LysR family genes, were likely to reduce Cr(VI) induced oxidative stress. In addition, real-time quantitative PCR was used to analyze the expression patterns of some Cr responsive genes. This study reported the first identification of Cr responsive genes, and inferred the underlying regulatory mechanisms of response to Cr(VI) stress in Pseudomonas sp. Cr13.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>35930609</pmid><doi>10.1371/journal.pone.0272528</doi><orcidid>https://orcid.org/0000-0003-1447-6117</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Amino acids Analysis Antioxidants Biology and Life Sciences Bioremediation Carbohydrate metabolism Carbohydrates Chromium Contaminants Contamination DNA testing Efficiency Efflux Energy metabolism Enzymes Exploitation Genes Genetic aspects Health aspects Health hazards Heavy metals Hexavalent chromium Kinases Laboratories Medicine and Health Sciences Metabolism Metals Microorganisms Mineral resources Oxidative stress Pathogenicity Pathogens Pathways Physical Sciences Physiology Pollution control Pseudomonas R&D Regulatory mechanisms (biology) Research & development Resource exploitation Sediment pollution Signal transduction Soil contamination Soil pollution Toxicity Transcriptomes |
| title | Identification of differentially expressed genes for Pseudomonas sp. Cr13 stimulated by hexavalent chromium |
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